The top scorer at the 1966 Cup also urged the media and public not to be too hard on England's Wayne Rooney and Portugal's Cristiano Ronaldo, who he said had tried but failed to reach their full potential in South Africa.
Eusebio and Germany's Gerd Muller, Golden Boot winner at the 1970 World Cup, picked Argentina striker Gonzalo Higuain, Spain's David Villa and Thomas Muller of Germany to fight it out for the 2010 top scorer award.
"I have no doubt that this little player who happens to be Argentinean, Messi, will be the best player of this tournament," he told reporters in Johannesburg.
"Unfortunately for Portugal, Cristiano Ronaldo did not do very well in this championship, but I am not going to condemn him for that," he said.
"I have also played in the past and I can understand players are in good or bad form."
Portugal lost to Spain in the second round, with Ronaldo, World Player of the Year in 2008, scoring just one goal which came during the team's 7-0 rout of North Korea.
"I believe Portugal played very well, we were beaten by Spain, by 1-0, and a very doubtful goal," he said.
Eusebio also defended Brazil's Kaka for being sent off against Ivory Coast for a second yellow card after allegedly elbowing Abdelkader Keita, saying he fell foul of the antics of other players and a "sleeping" linesman.
"I know Kaka very well, he is a true professional ... in this particular case I saw Kaka being provoked by the other player, I didn't see him touch the other player," he said.
"What I believe also is that maybe the linesman shouldn't fall asleep."
